diff --git a/.github/workflows/compile-msvc.yml b/.github/workflows/compile-msvc.yml index 216f465568..3ec5fc4cb0 100644 --- a/.github/workflows/compile-msvc.yml +++ b/.github/workflows/compile-msvc.yml @@ -3,9 +3,11 @@ name: "Native Windows Compilation and Unit Tests" on: push: - branches: [ develop ] + branches: + - develop pull_request: - branches: [ $default-branch ] + branches: + - develop workflow_dispatch: diff --git a/.github/workflows/unittest-macos.yml b/.github/workflows/unittest-macos.yml index aba0570f2b..2d29eac83e 100644 --- a/.github/workflows/unittest-macos.yml +++ b/.github/workflows/unittest-macos.yml @@ -3,9 +3,11 @@ name: "Unittest for MacOS" on: push: - branches: [ develop ] + branches: + - develop pull_request: - branches: [ $default-branch ] + branches: + - develop workflow_dispatch: diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt index aaa0885072..28c3d6c027 100644 --- a/cmake/CMakeLists.txt +++ b/cmake/CMakeLists.txt @@ -376,6 +376,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR) pkg_depends(CG-DNA MOLECULE) pkg_depends(CG-DNA ASPHERE) pkg_depends(ELECTRODE KSPACE) +pkg_depends(EXTRA-MOLECULE MOLECULE) # detect if we may enable OpenMP support by default set(BUILD_OMP_DEFAULT OFF) diff --git a/cmake/Modules/LAMMPSUtils.cmake b/cmake/Modules/LAMMPSUtils.cmake index 9f624fc007..9b75209e16 100644 --- a/cmake/Modules/LAMMPSUtils.cmake +++ b/cmake/Modules/LAMMPSUtils.cmake @@ -110,14 +110,16 @@ function(FetchPotentials pkgfolder potfolder) math(EXPR plusone "${blank}+1") string(SUBSTRING ${line} 0 ${blank} pot) string(SUBSTRING ${line} ${plusone} -1 sum) - if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot}) + if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}") file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum) endif() if(NOT sum STREQUAL oldsum) - message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}") - file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}" + message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}") + string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}") + file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" EXPECTED_HASH MD5=${sum} SHOW_PROGRESS) - file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR}) + file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}") + file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}") endif() endforeach() endif() diff --git a/cmake/Modules/Packages/MDI.cmake b/cmake/Modules/Packages/MDI.cmake index d873c8f6d1..8f7c87b684 100644 --- a/cmake/Modules/Packages/MDI.cmake +++ b/cmake/Modules/Packages/MDI.cmake @@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al if(DOWNLOAD_MDI) message(STATUS "MDI download requested - we will build our own") - set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball") - set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball") + set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball") + set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball") mark_as_advanced(MDI_URL) mark_as_advanced(MDI_MD5) enable_language(C) diff --git a/cmake/presets/clang.cmake b/cmake/presets/clang.cmake index a0d654ad35..f1964f3e0f 100644 --- a/cmake/presets/clang.cmake +++ b/cmake/presets/clang.cmake @@ -3,6 +3,13 @@ # prefer flang over gfortran, if available find_program(CLANG_FORTRAN NAMES flang gfortran f95) set(ENV{OMPI_FC} ${CLANG_FORTRAN}) +get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME) +if (_tmp_fc STREQUAL "flang") + set(FC_STD_VERSION "-std=f2018") + set(BUILD_MPI OFF) +else() + set(FC_STD_VERSION "-std=f2003") +endif() set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE) set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE) @@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) -set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE) -set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE) -set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE) +set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE) set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE) diff --git a/doc/lammps.1 b/doc/lammps.1 index f1a3d0f2f9..e4f0f2a9eb 100644 --- a/doc/lammps.1 +++ b/doc/lammps.1 @@ -1,7 +1,7 @@ -.TH LAMMPS "1" "3 August 2022" "2022-8-3" +.TH LAMMPS "1" "15 September 2022" "2022-9-15" .SH NAME .B LAMMPS -\- Molecular Dynamics Simulator. Version 3 August 2022 +\- Molecular Dynamics Simulator. Version 15 September 2022 .SH SYNOPSIS .B lmp diff --git a/doc/src/Bibliography.rst b/doc/src/Bibliography.rst index 9f3591dcde..dff457836c 100644 --- a/doc/src/Bibliography.rst +++ b/doc/src/Bibliography.rst @@ -1373,7 +1373,7 @@ Bibliography Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002). **(Ziegler)** - J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985. + J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985. **(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319. diff --git a/doc/src/Commands_all.rst b/doc/src/Commands_all.rst index 5e309c3ed0..d7b1609619 100644 --- a/doc/src/Commands_all.rst +++ b/doc/src/Commands_all.rst @@ -15,7 +15,9 @@ General commands ================ -An alphabetic list of general LAMMPS commands. +An alphabetic list of general LAMMPS commands. Note that style +commands with many variants, can be more easily accessed via the small +table above. .. table_from_list:: :columns: 5 @@ -61,6 +63,7 @@ An alphabetic list of general LAMMPS commands. * :doc:`kspace_modify ` * :doc:`kspace_style ` * :doc:`label